Actually I echo the same thoughts. Most holds I have no problem with finding the balance. But 2 I have some trouble with.

Shihonage and Sankyo.

I know it can be done without pain to the partner. I know I'm only trying to take their balance. I just don't know how to hold it without some discomfort on uke's part, not without losing control of uke anyway.

Discomfort occurs at Uke's wrist. Not shoulders or elbows etc.
Would welcome any insights.

My take fwiw. Pain in the wrist implies you haven't taken their balance and only have a "wrist" lock of sorts. The goal isn't controlling the wrist but everything else. Don't focus on the wrist but focus on taking their center away well before. Done correctly the shihonage and sankyo are simply controls as you continue to remove their balance. No pain necessary. If you stop and they regain balance, well, it becomes much harder to hold either of those two without delivering pain to get them off again. But if you're in a good flow with their balance taken initially, you can complete both without ever reverting to pain compliance again assuming you prevent them from regaining a balanced state.